Traditional tools for computer-based editing of three-dimensional models are surface based. Often, a model is represented as a collection of surface elements such as polygons or NURBS. Such tools support aggregation, repositioning and deformation of models readily, but do not lend themselves to topological modifications such as punching holes. These models also do not readily provide a watertight model, that is, one that unambiguously separates inside from outside at every point in space. For example, a collection of surface elements can leave an unfilled hole in the model, or two surface elements can intersect in a way that makes inside and outside classification unclear.